Publications

Awwad SW, Doyle C, Coulthard J, Bader AS, Gueorguieva N, Lam S, Gupta V, Belotserkovskaya R, Tran TA, Balasubramanian S, Jackson SP.

Nature Communications 16(1):480

ATR plays key roles in cellular responses to DNA damage and replication stress, a pervasive feature of cancer cells. ATR inhibitors (ATRi) are in clinical development for treating various cancers, including those with high replication stress, such as is elicited by ARID1A deficiency, but the cellular mechanisms that determine ATRi efficacy in such backgrounds are unclear. Here, we have conducted unbiased genome-scale CRISPR screens in ARID1A-deficient and proficient cells treated with ATRi.

Gang Goh C, Bader AS, Tran T-A, Belotserkovskaya R, D’Alessandro G and Jackson SP.

Nucleic Acids Research, gkae1163

HAP1 is a near-haploid human cell line commonly used for mutagenesis and genome editing studies due to its hemizygous nature. We noticed an unusual hypersensitivity of HAP1 to camptothecin, an antineoplastic drug that stabilizes topoisomerase I cleavage complexes (TOP1ccs). We have attributed this hypersensitivity to a deficiency of TDP1, a key phosphodiesterase involved in resolving abortive TOP1ccs.

Carnie CJ, Jackson SP and Stingele J.

Trends in Cell Biology 35(4), 316-329

DNA–protein crosslinks (DPCs) are highly toxic DNA lesions that are relevant to multiple human diseases. They are caused by various endogenous and environmental agents, and from the actions of enzymes such as topoisomerases. DPCs impede DNA polymerases, triggering replication-coupled DPC repair. Until recently the consequences of DPC blockade of RNA polymerases remained unclear. New methodologies for studying DPC repair have enabled the discovery of a transcription-coupled (TC) DPC repair pathway.

Lam S, Thomas JC and Jackson SP.

Genome Medicine 16:139 (2024)

Background CRISPR-Cas9 technology has revolutionised genetic screens and can inform on gene essentiality and chemo-genetic interactions. It is easily deployed and widely supported with many pooled CRISPR libraries available commercially. However, discrepancies between the reference genomes used in the design of those CRISPR libraries and the cell line under investigation can lead to loss of signal or introduction of bias. The problem is particularly acute when dealing with variant cell lines such as cancer cell lines.

Results Here, we present an algorithm, EXOme-guided Re-annotation of nuCleotIde SEquences (Exorcise), which uses sequence search to detect and correct mis-annotations in CRISPR libraries.

Lim JKM, Samiei A, Delaidelli A, de Santis JO, Brinkmann V, Carnie CJ, Radiloff D, Hruby L, Kahler A, Cran J, Leprivier G, Sorensen PH.

Cell Death & Disease 15(7):501.

Eukaryotic elongation factor 2 (eEF2) kinase (eEF2K) is a stress-responsive hub that inhibits the translation elongation factor eEF2, and consequently mRNA translation elongation, in response to hypoxia and nutrient deprivation. EEF2K is also involved in the response to DNA damage but its role in response to DNA crosslinks, as induced by cisplatin, is not known. Here we found that eEF2K is critical to mediate the cellular response to cisplatin.

Carnie CJ, Götz MJ, Palma-Chaundler CS, Weickert P, Wanders A, Serrano-Benitez A, Li HY, Gupta V, Awwad SW, Blum CJ, Sczaniecka-Clift M, Cordes J, Zagnoli-Vieira G, D'Alessandro G, Richards SL, Gueorguieva N, Lam S, Beli P, Stingele J, Jackson SP.

EMBO Journal 43, 2397 - 2423

The nucleoside analogue decitabine (or 5-aza-dC) is used to treat several haematological cancers. Upon its triphosphorylation and incorporation into DNA, 5-aza-dC induces covalent DNA methyltransferase 1 DNA-protein crosslinks (DNMT1-DPCs), leading to DNA hypomethylation. However, 5-aza-dC's clinical outcomes vary, and relapse is common. Using genome-scale CRISPR/Cas9 screens, we map factors determining 5-aza-dC sensitivity.

Carnie CJ, Acampora AC, Bader AS, Erdenebat C, Zhao S, Bitensky E, van den Heuvel D, Parnas A, Gupta V, D'Alessandro G, Sczaniecka-Clift M, Weickert P, Aygenli F, Götz MJ, Cordes J, Esain-Garcia I, Melidis L, Wondergem AP, Lam S, Robles MS, Balasubramanian S, Adar S, Luijsterburg MS, Jackson SP, Stingele J.

Nature Cell Biology 26, 797–810.

Covalent DNA-protein cross-links (DPCs) are toxic DNA lesions that block replication and require repair by multiple pathways. Whether transcription blockage contributes to the toxicity of DPCs and how cells respond when RNA polymerases stall at DPCs is unknown. Here we find that DPC formation arrests transcription and induces ubiquitylation and degradation of RNA polymerase II.

Adams DJ, Barlas B, McIntyre RE, Salguero I, van der Weyden L, Barros A, Vicente JR, Karimpour N, Haider A, Ranzani M, Turner G, Thompson NA, Harle V, Olvera-León R, Robles-Espinoza CD, Speak AO, Geisler N, Weninger WJ, Geyer SH, Hewinson J, Karp NA; Sanger Mouse Genetics Project; Fu B, Yang F, Kozik Z, Choudhary J, Yu L, van Ruiten MS, Rowland BD, Lelliott CJ, Del Castillo Velasco-Herrera M, Verstraten R, Bruckner L, Henssen AG, Rooimans MA, de Lange J, Mohun TJ, Arends MJ, Kentistou KA, Coelho PA, Zhao Y, Zecchini H, Perry JRB, Jackson SP, Balmus G.

Nature 627(8002):130-136

Genomic instability arising from defective responses to DNA damage or mitotic chromosomal imbalances can lead to the sequestration of DNA in aberrant extranuclear structures called micronuclei (MN). Although MN are a hallmark of ageing and diseases associated with genomic instability, the catalogue of genetic players that regulate the generation of MN remains to be determined. Here we analyse 997 mouse mutant lines, revealing 145 genes whose loss significantly increases (n = 71) or decreases (n = 74) MN formation, including many genes whose orthologues are linked to human disease.